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v1.0.0 beta4

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@blahah blahah released this 05 Jun 19:03
· 98 commits to master since this release
v1.0.0.beta4
820833c

screenshot 2014-10-17 11 22 27

transrate v1.0.0 beta 4

This is the fourth beta release of transrate v1. Please report any bugs on the issue tracker. Documentation for this release is on the transrate website: http://hibberdlab.com/transrate/.

Installation

Simple install

This is the simplest option if you just want to use transrate from the command-line...

Download one of the binaries linked below, unpack it, and add it to your PATH.

Advanced/developer install

This is the option you need if you want to develop code that uses transrate as a library...

$ gem install --pre transrate --version 1.0.0.beta4
$ transrate --install-deps

Changes

If you are updating from a version below v1, please see the release notes for v1.0.0.alpha1.

Changelog

beta4

  • We've updated our Salmon dependency to v0.4.0, which brings an awesome speed increase, especially for small datasets, as well as some improvement in accuracy for our read metrics.
  • Fixed a bug in --install-deps where it would always try to install all the dependencies
  • Improved handling of FASTA input edge-cases and unusual formatting
  • Better handling and reporting of errors and crashes in the dependencies
  • A big improvement to reference-based metrics when comparing to a reference that has repetitive sequences. Users should now see considerably higher reference coverage in some places (before, BLAST was masking out repetitive regions). Thanks to Nick Schurch and Chris Cole at Dundee for their analysis that led to discovering this issue.
  • Some command-line arguments have been reordered and their short-names changed, so now --right has -r for short and --reference has -a for short. Thanks to Matt Macmanes for highlighting this.

beta3

  • Transrate will automatically choose the optimal set of contigs from an assembly, maximising both the quality of the contigs and the proportion of the read evidence that is used. It now reports the raw assembly score as well as the optimised assembly score. The optimal assembly is found in good.*.fa
  • Transrate can now merge assemblies with the --merge-assemblies command, choosing the optimal set of contigs from all the input assemblies
  • Some great improvements to Salmon have been included in this release
  • Transrate now estimates the insert size distribution from the reads
  • Transrate is now distributed as a binary package (available for linux 64bit, and osx). This should greatly simplify installation for most users.

beta2

  • We have moved to using Salmon for read assignment. This has brought a massive speedup over using eXpress, because Salmon can use any number of cores (while eXpress is restricted to 3), and Salmon is generally optimised for speed
  • We've managed to eliminate much of the IO bottleneck that was caused by processing BAM files, thanks to the collaboration of the Salmon developer
  • We've fixed some bugs in the SNAP aligner that we depend on
  • Minor bug fixes in basic contig metrics for unusual kinds of inputs
  • Improved error handling and logging
  • Improved dependency management, with fewer dependencies

Acknowledgements

  • Rob Patro, developer of Salmon, for his hard work on making Salmon work well with transrate
  • Users, especially Matt Macmanes, for diligent testing and bug reporting
  • The SNAP team for responding rapidly to our bug reports
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